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Pythium ultimum vs Tetrahymena thermophila LastZ results

Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) and Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Pythium ultimum was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterPythium ultimumTetrahymena thermophila
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,273 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium ultimum

Uncovered: 43,913,232 out of 44,913,582
Covered: 1,000,350 out of 44,913,582

Uncovered: 18,999,658 out of 19,826,256
Matches: 482,945 out of 19,826,256
Mismatches: 323,184 out of 19,826,256
Insertions: 20,469 out of 19,826,256
Identity over aligned base-pairs: 58.4%

Tetrahymena thermophila

Uncovered: 100,955,831 out of 103,014,375
Covered: 2,058,544 out of 103,014,375

Uncovered: 46,787,940 out of 48,193,658
Matches: 588,616 out of 48,193,658
Mismatches: 788,409 out of 48,193,658
Insertions: 28,693 out of 48,193,658
Identity over aligned base-pairs: 41.9%

Block size distribution

Size range All 5,273 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
20
83.0 bp
10 bp - 100 bp
1,120
86.6 kb
374
30.5 kb
100 bp - 1 kb
3,918
1.2 Mb
1,893
722.7 kb
1 kb - 10 kb
181
315.7 kb
376
773.9 kb
10 kb - 100 kb
34
849.4 kb
36
896.8 kb